Spain had surprisingly lost 1-0 to Switzerland in their opening game but moved to second place in Group H after claiming their first three points.
The game was pretty much one-sided as Vicente del Bosque's team got the upper hand right after the kickoff, with their opponents only trying to keep a clean sheet most of the time.
Spain's first opportunity fell to Fernando Torres when he tried to connect with a low cross but his tame effort didn't disturb the goalie.
After seven minutes, Villa released a delightful shot from around 30 yards that was denied by the crossbar.
Honduras became dangerous on the counter attack for a short while after 10 minutes. David Suazo had one of his side's very few chances but keeper Iker Casillas competently prevented him from scoring.
The misfiring Torres squandered a couple of clear-cut chances with a tame header and a shot that went wide.
Two minutes past the quarter-hour mark, Villa broke the deadlock single-handedly when he incredibly dribbled past a couple of challengers before hitting the top corner of the net with a curling drive.
The Real Madrid target added the second goal with a nice shot from outside the area that deflected off a challenger and into the net on 52 minutes.
Spain's Xavi Hernandez could have get his name on the score sheet too but failed to head a Jesus Navas cross despite being unmarked.
On 61 minutes, Navas won a penalty kick that Villa waste to miss out on a chance of completing a hat-trick.
Argentina's Gonzalo Higuain has been the only player to hit a treble in the 2010 World Cup thus far.
Spain remained in control for the rest of the match and carved out many scoring chances that could have resulted in more goals.
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تقرير: بايرن ميونيخ يتوصل لاتفاق لضم الإكوادوري أولايو
مؤتمر أرتيتا: جيسوس جاهز ومستعد للمشاركة أساسيا ضد كريستال بالاس
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